Science Literature

The announcement of an Earth-like planet in the "habitable zone" of the star Gliese 581 has stirred immense interest in the media and blogs around the world. This appears to be the news many have been waiting for. The Daily Mail announced: It "forced bookies to slash odds on the existence of alien beings", and "This remarkable discovery appears to confirm the suspicions of most astronomers that the universe is swarming with Earth-like worlds."
The planet is thought to have a mass 5 times that of the Earth and a diameter 50% larger. The host star is a red dwarf with a small diameter and a surface temperature of about 3300 K. The planet is 14 times closer to the star than Earth is to the sun, and a full orbit is completed every 13 days. Taking into account the reduced radiation from the star and the closeness of the planet, the surface temperature of the planet is estimated in the range 0-40 C. This is sufficient to say that it lies in the "habitable zone" or (more evocatively) the "Goldilocks zone" where temperatures are just right for life.
However, the situation is not as comfortable as it might seem. A planet so close to the sun will become tidally locked with one side constantly in light and he other in darkness. Since it has an elliptical orbit, the case of Mercury might be a useful analogy. The discoverers of the planet say: "A detailed study will also need to consider the possible tidal locking of the planetary rotation to the orbital period". The implication is that liquid water (if water actually exists) is highly unlikely: most will be either in water vapour form or locked up as ice. The only real "Goldilocks zone" is at the terminator, which is sunset for unbridled excitement about the discovery.
Another problem concerns the light falling on the planet. Since the star is quite cool, the radiation peaks in the infrared. The radiation energy is relatively low compared with white light, insufficient to break chemical bonds necessary for plant-based photosynthesis. Whilst bacteria on earth appear to be able to exploit energy from hydrothermal vents , they inhabit a world that is far from our experience. So, even if the new planet's atmosphere was "just right" (which is also doubtful), Earth-like plant life would be impossible.
So, although some have spoken of an "oasis in space" and a "treasure", we ought to consider this new planet as very hostile to life and focus our excitement and energies on the "Goldilocks zone" represented by our own Earth.

The HARPS search for southern extra-solar planets
XI. Super-Earths (5&8M) in a 3-planet system
S. Udry, X. Bonfils, X. Delfosse, T. Forveille, M. Mayor, C. Perrier, F. Bouchy, C. Lovis, F. Pepe, D. Queloz, and J.-L. Bertaux.
Astronomy & Astrophysics, accepted for publication

Abstract. This Letter reports on the detection of two super-Earth planets in the Gl 581 system, already known to harbour a hot Neptune. One of the planets has a mass of 5M_ and resides at the "warm" edge of the habitable zone of the star. It is thus the known exoplanet which most resembles our own Earth. The other planet has a 7.7M_ mass and orbits at 0.25AU from the star, close to the "cold" edge of the habitable zone. These two new light planets around an M3 dwarf further confirm the formerly tentative statistical trend for i) many more very low-mass planets being found around M dwarfs than around solar-type stars and ii) low-mass planets outnumbering Jovian planets around M dwarfs.

See also:

Schilling, G. Exoplanets: Habitable, But Not Much Like Home, Science 316, 27 April 2007: 528.
For the first time, astronomers have found an Earth-like planet that could be habitable. Like an oasis in space, the rocky world, possibly covered with oceans, orbits a puny red dwarf star just over 20 light-years away in the constellation Libra. "On the treasure map of the universe, one would be tempted to mark this planet with an X," says team member Xavier Delfosse of Grenoble University in France. [snip]

Found 20 light years away: the New Earth
Daily Mail, 25th April 2007

The day after James Lake's interesting essay appeared in Nature, acknowledging that the origin of eukaryotes is one of the greatest enigmas in biology, he appeared as a co-signatory to some correspondence, attacking a paper published last year in Science. The paper maintained that hypotheses invoking genome fusion to explain the characteristic features of the eukaryote cell have failed. The authors reviewed recent data from proteomics and genome sequences and suggested that "eukaryotes are a unique primordial lineage".
The critics declared that this paper "delivered only biased opinions" and that the authors "arbitrarily pick and choose among available observations relating to sequence similarity". The end of their critique has this punchline: "Finally, and most disturbing, if contemporary eukaryotic cells are truly of "irreducible nature," as Kurland et al.'s title declares, then no stepwise evolutionary process could have possibly brought about their origin, and processes other than evolution must be invoked. Is there a hidden message in their paper?"
The authors of the paper have responded in a non-inflammatory way. They stand their ground. "Our view is that cellular and molecular biology, especially genomics, reveals signs of an ancient complexity of the eukaryotic cell." They conclude: "our primary conclusion is that there is good progress on understanding the complexity of the ancestral eukaryote cell".
The reason for drawing attention to this critique is that it provides a good example of how 'norms' are sustained within the scientific community. The critics cannot even consider the possibility of "stepwise evolutionary processes" failing to account for eukaryotes, and they have reacted with alarm. Thinking they have detected a hint of intelligent design (by the use the word "irreducible"), they declare this as "most disturbing" and talk about a "hidden message". This reaction moves the critique beyond the realm of scientific discourse into the world of ideological materialism. Those seeking to learn more about ID will do well to recognise the role played by worldviews held by those involved in the debates.

The Evolution of Eukaryotes (Letter )
William Martin, Tal Dagan, Eugene V. Koonin, Jonathan L. Dipippo, J. Peter Gogarten, James A. Lake.
Response by C. G. Kurland, Lesley J. Collins, and David Penny
Science 316, 27 April 2007: 542-543.

What can be said about the origin of the eukaryotic cell? "Until recently, everyone assumed, based on a single ribosomal RNA gene, that eukaryotes descended from archaebacteria - extremophilic prokaryotes distinct from 'true' bacteria, or eubacteria. Now we know that's not the case.' Genome studies reveal links with eubacteria as well as archaebacteria. There are also numerous losses of genes that are puzzling: "But how did evolution come up with the strange distribution of eubacterial and archaebacterial genes we see in eukaryotes today?"
In passing, we must note that an explanation in terms of evolutionary theory is assumed as a 'given'. It is as though no other avenues need be explored.
A remarkable paradox is introduced thus: "Because eukaryotes are derived from archaebacteria and eubacteria, one might expect to find an archaebacterial and a eubacterial copy of each nuclear gene. But strangely, archaebacterial operational and eubacterial informational genes are almost completely absent from eukaryotes, even though the first eukaryote contained two sets of informational and operational genes."
The author, James Lake, uses the analogy of the Roman god Janus. "Like the two faces of the Roman god Janus, thought to represent the Moon and the Sun, the phylogenetic origins of informational and operational genes in eukaryotes are as different as night and day. Finding a gene distribution such as this is the statistical equivalent of finding that a coin tossed at night (Janus's archaebacterial face) always comes up heads (informational genes), and tossed during the day (Janus's eubacterial face) always comes up tails (operational genes)."
Lake then discusses possible explanations of the Janus paradox. He offers a possible explanation as to why the eubacterial informational genes disappeared, but that's as far as he goes. "Unfortunately, I have no good suggestion for why the archaebacterial operational genes were eliminated." He concludes: "How the eukaryotic cell came to be is one of the greatest enigmas in biology. It is a story so complex that no single gene can tell it. Only entire genomes can."
The more we look at eukaryotes, the more obvious it becomes that an evolutionary story of simple to complex is woefully inadequate. But will genome studies help? Last year, the authors of a research paper wrote: "we review recent data from proteomics and genome sequences suggesting that eukaryotes are a unique primordial lineage". Some paradoxes can only be solved by changing the paradigm: maybe the avenue to be explored is signposted "intelligent design".

Disappearing act
James A. Lake
Nature 446, 983, (26 April 2007) | doi:10.1038/446983a
The bizarre absence of certain gene classes in eukaryotes is key to understanding their evolution and complex links with prokaryotes.

See also:
Kurland, C.G., Collins, L.J. and Penny, D. Genomics and the Irreducible Nature of Eukaryote Cells, Science 312, 19 May 2006: 1011-1014.

Wing morphology has a profound effect on aerodynamic performance. Gliding birds such as swifts exploit their ability to morph their wings: "Extended wings are superior for slow glides and turns; swept wings are superior for fast glides and turns. This superiority is due to better aerodynamic performance - with the exception of fast turns. Swept wings are less effective at generating lift while turning at high speeds, but can bear the extreme loads."
New research has led to a more refined aerodynamicmodel, enhancing understanding and stimulating ideas for future developments in aircraft design. "Lentink says that these aircraft designs are crude compared with what the swifts can do, thanks to the engineering challenges involved. "The swifts are just better at it," he says, "The amount of feathers and muscle involved is challenging for us [to imitate].""
One might anticipate that research like this might stimulate thoughts about intelligent design. That is certainly the way engineers have to approach their work. The glide speeds at which the birds minimize energy expenditure have been determined. But one of the co-authors is quoted as saying: "They [swifts] have evolved an aerodynamic design for cheap flight". However, there is nothing in this research that suggests that these capabilities are evolved rather than intelligently designed. This comment linking design to an evolutionary origin is theory-laden and is actually a pointer to a socially-constructed 'reality' adopted by the researcher.

How swifts control their glide performance with morphing wings
D. Lentink, U. K. Muller, E. J. Stamhuis, R. de Kat, W. van Gestel, L. L. M. Veldhuis, P. Henningsson, A. Hedenstrom, J. J. Videler and J. L. van Leeuwen.
Nature 446, 1082-1085 (26 April 2007) | doi:10.1038/nature05733

Gliding birds continually change the shape and size of their wings1, 2, 3, 4, 5, 6, presumably to exploit the profound effect of wing morphology on aerodynamic performance7, 8, 9. That birds should adjust wing sweep to suit glide speed has been predicted qualitatively by analytical glide models2, 10, which extrapolated the wing's performance envelope from aerodynamic theory. Here we describe the aerodynamic and structural performance of actual swift wings, as measured in a wind tunnel, and on this basis build a semi-empirical glide model. By measuring inside and outside swifts' behavioural envelope, we show that choosing the most suitable sweep can halve sink speed or triple turning rate. Extended wings are superior for slow glides and turns; swept wings are superior for fast glides and turns. This superiority is due to better aerodynamic performance - with the exception of fast turns. Swept wings are less effective at generating lift while turning at high speeds, but can bear the extreme loads. Finally, our glide model predicts that cost-effective gliding occurs at speeds of 8-10 m s-1, whereas agility-related figures of merit peak at 15-25 m s-1. In fact, swifts spend the night ('roost') in flight at 8-10 m s-1 (ref. 11), thus our model can explain this choice for a resting behaviour11, 12. Morphing not only adjusts birds' wing performance to the task at hand, but could also control the flight of future aircraft7.

See also:
Ledford, H. Wings in a wind tunnel show secrets of flight. Study of swifts could improve airplane designs.
news@nature.com, 25 April 2007 | doi:10.1038/news070423-7

For as long as many of us can remember, Lucy has been an iconic fossil in the story of human evolution. The discussions about walking erect have been extensive. Many regard the evidence as definitive. However, "Rak and colleagues studied 146 mature primate bone specimens, including those from modern humans, gorillas, chimpanzees and orangutans and found that the "ramus element" of the mandible connecting the lower jaw to the skull is like that of the robust forms". The presence of this morphology in both Australopithecus robustus and Australopithecus afarensis and its absence in modern humans has "cast doubt on the role of [Lucy] as a common ancestor." Like a baton passed from runner to runner, the distinctive bone does the job of "eliminating the possibility that Lucy and her kind are Man's direct ancestors."
So what can be said about Lucy? "The specimen was only 1.1 meters tall, estimated to weigh 29 kilograms and look somewhat like a common chimpanzee." Also, "the structure of Lucy's mandibular ramus closely matches that of gorillas", which was an unexpected find, because this does not fit the previous cladistic analyses of chimps, gorillas and humans.
It looks like this is an appropriate time to reappraise the way museums and textbooks present the story of human evolution.

Gorilla-like anatomy on Australopithecus afarensis mandibles suggests Au. afarensis link to robust australopiths
Yoel Rak, Avishag Ginzburg, and Eli Geffen
Proceedings of the National Academy of Sciences USA, April 17 2007, 104: 6568-6572, doi 10.1073/pnas.0606454104

Abstract: Mandibular ramus morphology on a recently discovered specimen of Australopithecus afarensis closely matches that of gorillas. This finding was unexpected given that chimpanzees are the closest living relatives of humans. Because modern humans, chimpanzees, orangutans, and many other primates share a ramal morphology that differs from that of gorillas, the gorilla anatomy must represent a unique condition, and its appearance in fossil hominins must represent an independently derived morphology. This particular morphology appears also in Australopithecus robustus. The presence of the morphology in both the latter and Au. afarensis and its absence in modern humans cast doubt on the role of Au. afarensis as a modern human ancestor. The ramal anatomy of the earlier Ardipithecus ramidus is virtually that of a chimpanzee, corroborating the proposed phylogenetic scenario.

See also:
Siegel-Itzkovich, J. Israeli researchers: 'Lucy' is not direct ancestor of humans, THE JERUSALEM POST, Apr. 16, 2007

Whilst some scholars recognise boundaries for scientific research, others strongly resist the thought that science has limits. One of the sensitive areas involves human consciousness and free agency. The authors of an essay on law and human behaviour write that "many contemporary neuroscientists assume that the essential ingredients of the human condition, including free will, empathy, and morality, are the calculable consequences of an immense assembly of neurons firing." This view "assumes that violence and antisocial behaviour emanate from a mechanistically determined brain". This effectively means that our sense of free agency is an illusion.
Whilst this stance man have legal implications (because of laws about diminished responsibility and even freedom from liability if declared legally insane), suffice to note here that our approach to the science of human behaviour has important ramifications.
What difference does this approach make to our thinking about humanity and society? "Clearly free will is a prerequisite for moral agency, and for society to run smoothly, we all need to believe that we are in full control of our actions." This sounds very much like living an illusion! To paraphrase: we cannot do without a sense of personal responsibility in order to have a society that works, but the neuroscientists know better (i.e. our behaviour is governed by neurons firing in our brains).
When we ask: 'how do we know?', we find out that the evidence is equivocal. No one has proved that the firings of neurons lead to "free-will, empathy and morality". The authors of the essay are right to use the word "assume". It is a major assumption that everything has a natural expanation: chance and necessity explains all (after Monod).
If these authors (and mechanistic neuroscientists) are right, then it is not only society that has to live an illusion. We ourselves have to live a delusion. We think we choose (but really it is only the firing of our neurons); we think we love (but this is just another form of brain signalling); and we think we know right from wrong (and this too is the product of neuron activity). Furthermore, our claims to be truth seekers are empty, because our response to truth is also an illusionary experience.
The authors write: "New studies of the criminal brain are likely to shape moral views on responsibility and free will, with possible impacts on how legal systems punish and treat criminals". If we are concerned about these issues, we need to look very carefully at the assumptions we bring to the science underpinning these studies.

Law, Responsibility, and the Brain
Dean Mobbs, Hakwan C. Lau, Owen D. Jones, Christopher D. Frith
PLoS Biol 5(4): e103 doi:10.1371/journal.pbio.0050103

Archaeological discoveries of traumatic injuries in primitive hominid skulls strongly hint that our species has a long history of violence. Despite repeated attempts throughout history, including efforts to eliminate violence through the imposition of criminal sanctions, we have yet to dispel our violent nature. Consequently, criminal violence remains a common feature of most societies. As policy-makers seek deeper understandings of criminally violent and anti-social behaviour, many contemporary neuroscientists assume that the essential ingredients of the human condition, including free will, empathy, and morality, are the calculable consequences of an immense assembly of neurons firing. Intuitively, this view opposes Cartesian dualism (i.e., the brain and mind are separate, but interacting, entities) and assumes that violence and antisocial behaviour emanate from a mechanistically determined brain.

"The rise of the central nervous system [CNS] in animal evolution has puzzled scientists for centuries." According to evolutionary theory, "Vertebrates, insects and worms evolved from the same ancestor, but their CNSs are different and were thought to have evolved only after their lineages had split during evolution." To gain an insight into what CNS of the last common ancestor of these groups might have been like, researchers selected for study the nervous system of a marine annelid worm called Platynereis dumerilii. "Platynereis can be considered a living fossil," says Arendt (who led the team), "it still lives in the same environment as the last common ancestors used to and has preserved many ancestral features, including a prototype invertebrate CNS."
"Our findings were overwhelming," says Alexandru Denes (who carried out the research in Arendt's lab). "The molecular anatomy of the developing CNS turned out to be virtually the same in vertebrates and Platynereis." The research paper expresses it thus: "Our comparative study of mediolateral neural patterning and neuron-type distribution in the developing trunk CNS of the annelid Platynereis revealed an unexpected degree of similarity to the mediolateral architecture of the developing vertebrate neural tube."
The implication is that something very like the vertebrate CNS existed in the putative common ancestor: "Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS, as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria."
So, the implication is that a highly complex nervous system existed in Precambrian organisms. "Such a complex arrangement could not have been invented twice throughout evolution, it must be the same system," adds Gaspar Jekely. "It looks like Platynereis and vertebrates have inherited the organisation of their CNS from their remote common ancestors."
This is interesting logic, because it links complexity with improbability. The greater the complexity, the less likely it is for processes governed by law or chance to produce it. Science built on naturalism has no other options available: complexity has to be the result of improbable interactions in nature. Design inferences are not permitted alongside inferences of law or chance. It is not acceptable to think that if it is too complex to have been 'invented' twice by evolution, it is also reasonable to conclude that it could not have been 'invented by evolution' even once.
Based on the research, the authors acknowledge that their findings "would imply that it was initially present also in the evolutionary lines leading to Drosophila, the nematode Caenorhabditis, and the enteropneust Saccoglossus. Yet it is clear from the available data that these animals are missing or have modified at least part of this pattern." Loss of complexity is a part of their story, which is a surprising result.
One cannot help notice that studies of this type keep pushing back the origin of complexity into the Precambrian, dominated until the Ediacaran by single-celled animals. Arguing that all this complexity is the product of mutation and natural selection becomes less and less convincing as we learn more about the data needing an explanation.

Molecular Architecture of Annelid Nerve Cord Supports Common Origin of Nervous System Centralization in Bilateria
Alexandru S. Denes, Gaspar Jekely, Patrick R.H. Steinmetz, Florian Raible, Heidi Snyman, Benjamin Prud'homme, David E.K. Ferrier, Guillaume Balavoine, and Detlev Arendt
Cell, Vol 129, 277-288, 20 April 2007

Summary: To elucidate the evolutionary origin of nervous system centralization, we investigated the molecular architecture of the trunk nervous system in the annelid Platynereis dumerilii. Annelids belong to Bilateria, an evolutionary lineage of bilateral animals that also includes vertebrates and insects. Comparing nervous system development in annelids to that of other bilaterians could provide valuable information about the common ancestor of all Bilateria. We find that the Platynereis neuroectoderm is subdivided into longitudinal progenitor domains by partially overlapping expression regions of nk and pax genes. These domains match corresponding domains in the vertebrate neural tube and give rise to conserved neural cell types. As in vertebrates, neural patterning genes are sensitive to Bmp signaling. Our data indicate that this mediolateral architecture was present in the last common bilaterian ancestor and thus support a common origin of nervous system centralization in Bilateria.

See also:
The origin of the brain lies in a worm
Researchers discover that the centralised nervous system of vertebrates is much older than expected
EMBL Press Release 20 April 2007

The iconic status of the bacterial flagellum as an irreducibly complex structure has stimulated interest among evolutionary biologists and an extensive literature. The latest is by Liu and Ochman who claim not only that the bacterial flagellum has originated in a stepwise manner from simple precursors, but also that "a single gene that underwent successive duplications and subsequent diversification during the early evolution of Bacteria."
ScienceNow has a report on this paper, with quotes drawn from the science community: "Complexity builds out of simplicity, and this is a well-documented argument for how that can happen," and "By testing the hypothesis of common ancestry of the flagellum in so many different species, the researchers clearly show these genes were derived from one another through gene duplication."
The major claim of the authors is to have traced the history of a set of core flagellum genes. "Our results show that flagellum originated very early, before the diversification of contemporary bacterial phyla, and evolved in a stepwise fashion through a series of gene duplication, loss and transfer events." They have adopted a methodology based on gene sequencing: "Comparisons of the complete genome sequences of flagellated bacteria revealed that the flagellum is based on an ancestral set of 24 core genes for which homologs are present in genomes of all bacterial phyla. The most striking finding from our analysis is that these core genes originated from one another through a series of duplications, an inference based on the fact that they still retain significant sequence homology."
So, have ID scientists got it wrong? The first point to be made is that the problem of actually forming the flagellum has not been addressed in the paper at all! There is no engagement with the challenge of irreducible complexity. Instead, this paper simply compares sequences of proteins, looking for similarities and differences in amino acid order. The analysis is concerned with sequence data, and the interpretation is dependent on the conceptual framework adopted by the researchers. In this case, the conceptual framework is Darwinism. The researchers have assumed that sequence similarity is related to ancestry, even though they cannot show that Darwinian processes produced the flagellum using their data set. This is a basic methodological point, and ID scholars have been making it for at least a decade. Consequently: 'Darwinism in - Darwinism out' sums up the findings.
There are many other detailed criticisms that can be made. Happily, a good start has been made here by Nick Matzke, who refers to "canine qualities" of the paper. By this he means that "there is nothing for it but to suck it up and declare this paper a dog." Of the claim that all flagellar proteins come from one gene, Matzke writes: "Frankly it is a flabbergasting thing to say, and I can't understand how it got published." Also: "There is just no way that the flagellum evolved by diversification of a single gene." However, Matzke misses the main methodological flaw in the research, which concerns their interpretation of sequence homologies in terms of descent with stepwise modification.
Jennifer Cutraro wrote that the study "not only answers an important question about the evolution of complex structures but also provides additional ammunition to counter arguments from evolution's foes." ID scientists are opposed to the 'just-so' stories and unwarranted extrapolations which are often found associated with evolutionary biology. By overstepping the mark so badly, perhaps this new paper will help people to understand the importance of paradigms in science and why critical issues are continually being overlooked.

Stepwise formation of the bacterial flagellar system
Renyi Liu and Howard Ochman
Proc. Natl. Acad. Sci. USA, 10.1073/pnas.0700266104, Published online before print April 16, 2007 [OPEN ACCESS ARTICLE]

Abstract: Elucidating the origins of complex biological structures has been one of the major challenges of evolutionary studies. The bacterial flagellum is a primary example of a complex apparatus whose origins and evolutionary history have proven difficult to reconstruct. The gene clusters encoding the components of the flagellum can include >50 genes, but these clusters vary greatly in their numbers and contents among bacterial phyla. To investigate how this diversity arose, we identified all homologs of all flagellar proteins encoded in the complete genome sequences of 41 flagellated species from 11 bacterial phyla. Based on the phylogenetic occurrence and histories of each of these proteins, we could distinguish an ancient core set of 24 structural genes that were present in the common ancestor to all Bacteria. Within a genome, many of these core genes show sequence similarity only to other flagellar core genes, indicating that they were derived from one another, and the relationships among these genes suggest the probable order in which the structural components of the bacterial flagellum arose. These results show that core components of the bacterial flagellum originated through the successive duplication and modification of a few, or perhaps even a single, precursor gene.

See also:

Cutraro, J., A Complex Tail, Simply Told, ScienceNOW Daily News, 17 April 2007

Matzke, N., Flagellum evolution paper exhibits canine qualities, Panda's Thumb, April 16, 2007

Behe, M. DARWINISM GONE WILD: Neither sequence similarity nor common descent address a claim of Intelligent Design, Evolution News & Views, 19 April 2007.

Reconstructions of ancient hominids are typically presented with no explanation of the principles on which the various bones are reassembled. Dr. Timothy Bromage is a paleoanthropologist who works on the biological principle "that the eyes, ears, and mouth must be in precise relationship to one another in all mammals." He claims to have found a rule that applies to all primates: "The angle created by drawing a line from the eye socket to the ear and then to the top back molar is always 45 degrees". Applying this to Homo rudolfensis (1470 Man) has challenged the previously accepted work. "Shifting the skull bones to conform to the rule pushes out the lower face and leads to a much smaller brain: about 575 cubic centimetres" instead of 750-775 cc. "Dr. Leakey produced a biased reconstruction based on erroneous preconceived expectations of early human appearance that violated principles of craniofacial development," said Dr. Bromage. His new reconstruction "shows a sharply protruding jaw and a brain less than half the size of a modern human". The first human-like skulls come with Homo ergaster and Homo erectus. This is exactly where many put the ape/homo line, and this new work reinforces the view that the gradualist model of human evolution is artificial and an imposition on the data.

New face for Kenya hominid?
Constance Holden
Science 316, 6 April 2007, 27.

See also:
Man's earliest direct ancestors looked more apelike than previously believed
EurekAlert, 24 March 2007.

"Photosynthetic complexes are exquisitely tuned to capture solar light efficiently, and then transmit the excitation energy to reaction centres, where long term energy storage is initiated." The problem has been one of understanding how 95%+ efficiencies are possible in a natural system.
The photosynthetic apparatus is constructed so that adjacent chlorophyll molecules have different energy levels. "When light shines on one of these molecules, an electron is momentarily excited before passing its energy over to a nearby molecule with a slightly lower energy level. In this way energy can flow "downhill" from energy level to energy level until it reaches the crucial "reaction centre" where the actual photosynthesis occurs. Scientists had assumed that the energy moves downhill in a "random walk", which is essentially an incoherent "hopping" between energy levels." But this mechanism does not yield the "extreme efficiency" of photosynthesis.
Researchers in the US have "discovered regular variations of signal that sustained for hundreds of femtoseconds, which the physicists interpreted as "quantum beats" coherently linking all the energy levels together." This "quantum trickery" has an analogy in "Grover's algorithm" (proposed in 1997) which determines "the fastest possible search of an unsorted database in quantum computation." With this mechanism, "vast areas of phase space can be sampled effectively to find the most efficient path for energy transfer."
Those involved in a quest for simplicity in the machinery of molecular biology are not having a very happy time. The story being uncovered is one of complexity in the details, as Michael Behe demonstrated in Darwin's Black Box. Knowing that quantum paths have been used in photosynthesis, the "primary energy source for almost all life on Earth", provides yet more grounds for making design inferences.

Evidence for wavelike energy transfer through quantum coherence in photosynthetic systems
Gregory S. Engel, Tessa R. Calhoun, Elizabeth L. Read, Tae-Kyu Ahn, Tomas Mancal, Yuan-Chung Cheng, Robert E. Blankenship and Graham R. Fleming.
Nature 446, 782-786 (12 April 2007) | doi:10.1038/nature05678

Abstract: Photosynthetic complexes are exquisitely tuned to capture solar light efficiently, and then transmit the excitation energy to reaction centres, where long term energy storage is initiated. The energy transfer mechanism is often described by semiclassical models that invoke 'hopping' of excited-state populations along discrete energy levels1, 2. Two-dimensional Fourier transform electronic spectroscopy3, 4, 5 has mapped6 these energy levels and their coupling in the Fenna-Matthews-Olson (FMO) bacteriochlorophyll complex, which is found in green sulphur bacteria and acts as an energy 'wire' connecting a large peripheral light-harvesting antenna, the chlorosome, to the reaction centre7, 8, 9. The spectroscopic data clearly document the dependence of the dominant energy transport pathways on the spatial properties of the excited-state wavefunctions of the whole bacteriochlorophyll complex6, 10. But the intricate dynamics of quantum coherence, which has no classical analogue, was largely neglected in the analyses-even though electronic energy transfer involving oscillatory populations of donors and acceptors was first discussed more than 70 years ago11, and electronic quantum beats arising from quantum coherence in photosynthetic complexes have been predicted12, 13 and indirectly observed14. Here we extend previous two-dimensional electronic spectroscopy investigations of the FMO bacteriochlorophyll complex, and obtain direct evidence for remarkably long-lived electronic quantum coherence playing an important part in energy transfer processes within this system. The quantum coherence manifests itself in characteristic, directly observable quantum beating signals among the excitons within the Chlorobium tepidum FMO complex at 77 K. This wavelike characteristic of the energy transfer within the photosynthetic complex can explain its extreme efficiency, in that it allows the complexes to sample vast areas of phase space to find the most efficient path.

See also:

Making photosynthesis tick (Editor's summary, Nature 446,(12 April 2007).

Sension, R.J. Quantum path to photosynthesis, Nature 446, 782-786 (12 April 2007) | doi:10.1038/446740a
Knowing how plants and bacteria harvest light for photosynthesis so efficiently could provide a clean solution to mankind's energy requirements. The secret, it seems, may be the coherent application of quantum principles.

Cartwright, J. Photosynthesis takes a leaf out of the quantum book, PhysicsWeb, April 13 2007.
Quantum computers and blades of grass have more in common than you might think. Physicists in the US have shown that electrons involved in photosynthesis reactions "sample" different energy-level routes in much the same way quantum-computer algorithms can - at least in theory - quickly search through unsorted databases. The researchers claim that the discovery could explain how photosynthesis can proceed at efficiencies unparalleled in manmade solar cells.

Two outspoken defenders of Darwinism and critics of ID have contributed a Policy Forum piece to Science on how scientists should contribute to "highly contested issues". They identify three cases for consideration: human-induced global warming, evolution and ID, and embryonic stem cells. In each case, they suggest that the thinking of scientists has converged towards an unambiguous position. But, they write: "Research shows that people are rarely well enough informed or motivated to weigh competing ideas and arguments." We live in societies where political and religious ideologies act as screens to distort the messages they hear. So we need to develop skills of communicating: "scientists must learn to actively "frame" information to make it relevant to different audiences". "Frames organize central ideas, defining a controversy to resonate with core values and assumptions".
These two communicators realise that they are advancing ideas that could be seen as manipulation of the media to keep the masses submissive. They conclude: "Some readers may consider our proposals too Orwellian, preferring to safely stick to the facts. Yet scientists must realize that facts will be repeatedly misapplied and twisted in direct proportion to their relevance to the political debate and decision-making. In short, as unnatural as it might feel, in many cases, scientists should strategically avoid emphasizing the technical details of science when trying to defend it."
The fundamental problem evident here is that the authors have failed to grasp that all three of their illustrative cases relate to contested issues within science, as well as having major ramifications for society. There is a significant debate as to whether global warming is human-induced; there is a community of scientists who dissent from Darwinism, many of whom are ID advocates; and there are good scientific reasons for focussing research on adult stem cells rather than embryonic stem cells. The authors are seeing these controversies through their personal ideological "frame".
They qualify their advice on strategy using these words: "without misrepresenting scientific information". However, their analysis of the controversial issues reveals that they have already misrepresented scientific information - by failing to acknowledge the reality of scientific debate and by linking dissent only to political and religious agendas. This is a sure sign of Orwellian control police and a sad day for science.

Framing Science
Matthew C. Nisbet and Chris Mooney
Science 315, 6 April 2007: 56

Issues at the intersection of science and politics, such as climate change, evolution, and embryonic stem cell research, receive considerable public attention, which is likely to grow, especially in the United States as the 2008 presidential election heats up.

Although hagfish have no jaws and no vertebrae, they do have other characters that identify them as fish. These traits make them an interesting candidate for being in some way transitional between chordates and vertebrates. Research has not been helped by the extreme difficulty of breeding these animals in captivity. A recent study has, however, succeeded in analyzing hagfish embryos and late-stage specimens have revealed the presence of a neural crest, a distinctive characteristic of vertebrates. The neural crest is a remarkable tissue that differentiates into a great variety of specialist cells, and is consequently very important for developmental biologists.
From an evolutionary perspective, this implies that the common ancestor of vertebrates would have possessed a neural crest. The authors suggest that "the neural crest probably existed as a population of delaminating and migrating cells in the common ancestor of the entire vertebrate clade, and thus its origin should be sought in non-vertebrate chordates."
Where do these animals fit into our understanding of living things? Are they (as many like to think) primitive vertebrates? This question has not been answered by palaeontology, because the earliest hagfishes are very similar to living forms. Two possibilities have been suggested: they could be primitive vertebrates (lacking vertebrae and jaws), or they could be degenerate organisms after losing several vertebrate characters (an option which also gets support from DNA and RNA sequencing). These possibilities are discussed by Janvier in a useful "News & Views" essay. In his judgment, "with this discovery, hagfishes become more 'conventional' vertebrates". The issues now are clearer than they were. But the big question remains unresolved. "Further analyses of the developmental genetics of hagfish embryos might enable us to discover whether hagfish anatomy is primitive or degenerate, and may help in reconstructing the theoretical common ancestor to all vertebrates."
At present, it is necessary to acknowledge that this theoretical "common ancestor to all vertebrates" is highly elusive. The search itself is theory-driven: based on the conviction that there must be a common ancestor. The authors say that their work "opens up new approaches to clarifying the evolutionary history of vertebrates", and this is true. However, should we adopt the restrictive approach that insists on a common ancestor in a Darwinian sense? Is there not scope here for an information-perspective on the basic types of life?

Hagfish embryology with reference to the evolution of the neural crest
Kinya G. Ota, Shigehiro Kuraku & Shigeru Kuratani
Nature 446, 672-675 (5 April 2007) | doi:10.1038/nature05633

Hagfish, which lack both jaws and vertebrae, have long been the subject of intense interest owing to their position at a crucial point in the evolutionary transition to a truly vertebrate body plan1, 2, 3, 4. However, unlike the comparatively well characterized vertebrate agnathan lamprey, little is known about hagfish development. The inability to analyse hagfish at early embryonic stages has frustrated attempts to resolve questions with important phylogenetic implications, including fundamental ones relating to the emergence of the neural crest1, 5, 6. Here we report the obtainment of multiple pharyngula-stage embryos of the hagfish species Eptatretus burgeri and our preliminary analyses of their early development. We present histological evidence of putative neural crest cells, which appear as delaminated cells that migrate along pathways corresponding to neural crest cells in fish and amphibians2, 7, 8, 9, 10, 11. Molecular cloning studies further revealed the expression of several regulatory genes, including cognates of Pax6, Pax3/7, SoxEa and Sox9, suggesting that the hagfish neural crest is specified by molecular mechanisms that are general to vertebrates. We propose that the neural crest emerged as a population of de-epithelialized migratory cells in a common vertebrate ancestor, and suggest that the possibility of classical and molecular embryology in hagfish opens up new approaches to clarifying the evolutionary history of vertebrates.

See also:
Janvier, P. Born-again hagfishes, Nature 446, 622-623 (5 April 2007) | doi:10.1038/nature05712
Abstract: The strange, slimy creatures called hagfishes are of abiding interest to students of vertebrate evolution: just where do they fit in? Investigations of hagfish development take the story forward.

Comb jellies are some of the most evocative marine animals, with transparent tissues enclosing blue combs in constant motion. Their fossil record goes back to the Cambrian, where they appear with essentially modern forms. A new research paper documents "an exquisitely preserved late-stage embryo of a ctenophore ("comb jelly")" in sediments that are right at the base of the Cambrian. "This specimen represents the earliest firm evidence of the Ctenophora now known".
"The ctenophoran affinities of this embryo are firmly supported by the presence of eight sets of comb rows and comb plates, and of meridional and aboral canals, all having the same relative positions as those in modern ctenophores. The presence of an adult body plan and of adult-like structures, even in its prehatching embryonic condition, suggests that this ancient ctenophore embryo would have likely directly matured into a planktonic juvenile like that of most modern ctenophores.[. . .] Its lack of tentacles and the presence of branched meridional canals, however, are characters shared by the embryos of extant beroidian ctenophores, with which this fossil therefore seems more closely allied."
The authors consider the common ancestor of these organisms. Their discovery rules out several previously proposed candidates. Links with Precambrian faunas are also rejected: "the suggestion by Shu et al. that the Ctenophora occupies an intermediate evolutionary position between sponges and cnidarians is inconsistent with numerous lines of evidence, both anatomical and molecular."
So we are left with the thought that the earliest ctenophore was rather like "extant beroidian ctenophores" and some of us might question whether there ever was a branch linking ctenophores to the elusive Darwinian Tree of Life.

Raman spectra of a Lower Cambrian ctenophore embryo from southwestern Shaanxi, China
Jun-Yuan Chen, J. William Schopf, David J. Bottjer, Chen-Yu Zhang, Anatoliy B. Kudryavtsev, Abhishek B. Tripathi, Xiu-Qiang Wang, Yong-Hua Yang, Xiang Gao, and Ying Yang.
Proc. Natl. Acad. Sci. USA, (10 April, 2007), 104(15), 6289-6292. DOI: 10.1073/pnas.0701246104 (OPEN ACCESS ARTICLE)

The Early Cambrian (~540 million years old) Meishucun fossil assemblage of Ningqiang County (Shaanxi Province), China, contains the oldest complex skeletonized organisms known in the geological record. We here report the finding in this assemblage of an exquisitely preserved late-stage embryo of a ctenophore ("comb jelly"), its fine structure documented by confocal laser scanning microscopy and shown by Raman spectroscopy to be composed of carbonaceous kerogen permineralized in apatite. In its spheroidal morphology, the presence of eight comb rows and the absence of tentacles, this embryo resembles an adult ctenophore (Maotianoascus octonarius) known from the immediately younger Chengjiang fauna of Yunnan, China. The oldest ctenophore and the only embryonic comb jelly known from the fossil record, this exceptionally well preserved specimen provides important clues about the early evolution of the phylum Ctenophora and of metazoans in general.

Despite the tremendous range of size and shape, terrestrial animals engaged in straight-line running can be modelled successfully. "Using simple mathematical models such as the SLIP model to describe movement allows for design and function to be understood in terms of overall mechanical task constraints." Add to this manoeuvring, and the story gets much more complicated. Stops, starts and changes in direction are much more of a challenge.
Past work in this area has involved cockroaches and humans. Newly reported research concerns ostriches. At first glance, these large birds might seem unlikely runners, but they are actually capable of taking on racehorses and certainly outmanoeuvring predators. Compared with humans, the centre of mass is higher, they have long spindly legs and long necks, and their heads are small. Not only can they run much faster than humans, they look remarkably graceful, even when changing direction. They do run turn differently: "When humans execute 30 degreees sidestep and crossover cuts, braking forces are 26% of Fpmax compared to 6-11% for ostriches executing 15-20 degree turns. Moreover, whereas humans generated almost exclusively braking forces during sidesteps and crossovers, 40% of the net forces observed during turns for ostriches were acceleratory." How do they achieve this remarkable performance?
"Most of the differences between ostriches and humans were explained by differences in body morphology. Ostrich morphology is appropriate for effective maneuvers that require minimal acceleratory or braking forces." "These results suggest that, with an appropriately designed morphological system, maneuvers can be executed with minimal changes to running dynamics." "In summary, ostrich morphology is appropriate for maneuvering without requiring large braking or acceleratory forces."
What stands out in these studies is the effectiveness of design thinking. Some will attribute this design to the powers of natural selection acting on genetic variations, with little or no direct evidence to support this hypothesis. However, there is another alternative, which is to be open to the possibility of this design being real, involving intelligent (rather than natural) agency. Ostriches have traditionally been considered the epitome of foolish behaviour, supposedly burying their heads in the sand. However, their running skills are outstanding and demonstrate superb design. One wonders whether heads are being buried in the sand when design inferences are excluded on ideological grounds from science.

Mechanics of cutting maneuvers by ostriches (Struthio camelus)
Devin L. Jindrich, Nicola C. Smith, Karin Jespers, and Alan M. Wilson
Journal of Experimental Biology, 2007 210: 1378-1390.

Abstract: We studied the strategies used by cursorial bipeds (ostriches) to maneuver during running. Eight ostriches were induced to run along a trackway and execute turns. Ground reaction forces and three-dimensional kinematics of the body and leg joints were simultaneously recorded, allowing calculation of joint angles and quasi-static net joint torques. Sidesteps, where the leg on the outside of the turn changes the movement direction, and crossovers using the inside leg, occurred with nearly equal frequency. Ostriches executed maneuvers using a simple control strategy that required minimal changes to leg kinematics or net torque production at individual joints. Although ostriches did use acceleration or braking forces to control body rotation, their morphology allowed for both crossovers and sidesteps to be accomplished with minimal net acceleratory/braking force production. Moreover, body roll and ab/adduction of the leg shifted the foot position away from the turn direction, reducing the acceleratory/braking forces required to prevent under- or over-rotation and aligning the leg with the ground reaction force.

See also:
Clare, S. BUILT TO RUN, Journal of Experimental Biology, 210, 0i (March 31, 2007)